{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/simlr-a-tool-for-large-scale-genomic-analyses","title":"SIMLR: A Tool for Large-Scale Genomic Analyses by Multi-Kernel Learning","arxiv_id":"1703.07844","date":"2017-03-21","proceeding":null,"authors":["Bo Wang","Daniele Ramazzotti","Luca De Sano","Junjie Zhu","Emma Pierson","Serafim Batzoglou"],"abstract":"We here present SIMLR (Single-cell Interpretation via Multi-kernel LeaRning),\nan open-source tool that implements a novel framework to learn a\nsample-to-sample similarity measure from expression data observed for\nheterogenous samples. SIMLR can be effectively used to perform tasks such as\ndimension reduction, clustering, and visualization of heterogeneous populations\nof samples. SIMLR was benchmarked against state-of-the-art methods for these\nthree tasks on several public datasets, showing it to be scalable and capable\nof greatly improving clustering performance, as well as providing valuable\ninsights by making the data more interpretable via better a visualization.\nAvailability and Implementation\n  SIMLR is available on GitHub in both R and MATLAB implementations.\nFurthermore, it is also available as an R package on http://bioconductor.org.","url_abs":"http://arxiv.org/abs/1703.07844v2","url_pdf":"http://arxiv.org/pdf/1703.07844v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"simlr-a-tool-for-large-scale-genomic-analyses","repo_url":"https://github.com/BatzoglouLabSU/SIMLR","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[{"task_slug":"clustering","task_name":"Clustering"},{"task_slug":"dimensionality-reduction","task_name":"Dimensionality Reduction"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}